-----------------------
Start of variable list:
-----------------------
Sample_ID:
M9-MAA000907-3_11_M-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/SRR
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Oct 12 19:41:26 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790707
Current job name : Step_02_M9-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790707.1.linga

Loading required modules...


List files in scratch directory:

total 12M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 78 root   root      108K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 M9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 5.9M Oct 12 19:41 SRR6576610_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 5.8M Oct 12 19:41 SRR6576610_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576610_1.fastq <==
@SRR6576610.1 1/1
GTGACGAAATATAACAATACAGGACTCTTTCGAGACCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGT
+
FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576610.2 2/1
CGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576610.3 3/1
TTATAAAAATCCTTCGACTGGCGCATGTACGTTTGAAGGCATGAGTTGGAAACAGGGAAGATGGAAGTGTTAGGCTAGCCGGGCGATGGTGGCGCACGCC
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576610.4 4/1
GGCTAAGCTGACCTGGAACTCACAGAGATCCACCTGCCTCTACCTCCTGAGTGCTGGGATTAAAGGCATACACCATCACTGCCTGGCTTAACATTTTAAT
+
FFF-F-FFFFFFFFFFF8F8FFFFFFFF8FFFFF8FFFFFFFFF-FF-FFFFFFFFFFF-FFF-FFF-F-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576610.5 5/1
TCCTTGTAGTGGCTGACTTCCTGCTCCTCGGCCCCAAAGCTTCGCACAGTCTGCAGCCCTCCTACCGCCTCGCGCACCACCTGCCCCGCCTTGGCCACTG
+
FFFFF-FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FF-FFFFFFFFFFFFFFFF-F

==> SRR6576610_2.fastq <==
@SRR6576610.1 1/2
TTCTTGGACCGGCGCAATACGAATGCCCCCGGCCGTCCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCGTTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576610.2 2/2
CTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576610.3 3/2
ATCTTGAATGCTGGCATCCAAAGTTGTCTTAACTTCCATTTTGTTTTTCTATCTTGCTTCTTTCTATCTTCTATTCTTCGGCTTCCTACTACCTGTGCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF----FFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFF8
@SRR6576610.4 4/2
GACAATAGTCTGTTCAAGTGTGTGCTAGGTCTACAAATAGCACAGAACACCAGGATGTTAACTATATCCATTCCCAGACATCTGGGTGGAAAACAGGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576610.5 5/2
ACAGAACACTGATGAAGCGGTTGCTGAAGCTGTCCAGGCCGGACCTGCCTTTCCTCATAGCTGGCTTCTTCTTCCTTGTGGTGGCTGTGTGGGGGGAGAC
+
FFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFF-FFFFFFF-FF---F-F--FF-FFFFFFFFFF-FFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576610_1.fastq

Printing command:
fastqc --outdir SRR6576610_1.fastq

Analysis complete for SRR6576610_1.fastq

Processing SRR6576610_2.fastq

Printing command:
fastqc --outdir SRR6576610_2.fastq

Analysis complete for SRR6576610_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 60M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 82 root   root      108K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 M9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:41 SRR6576610_1.fastq
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:41 SRR6576610_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:47 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================